Tony Stark is left the sole survivor when his father's plane crashes. Now an orphan, he is presented with a questionable 'last request' of his father: live with the Rhodes and go to school. Encouraged by Pepper Potts and assisted by Jim Rhodes, the 16 year old genius begins to investigate the suspicious activities carried out by Obadiah Stane, the new C.E.O. of Stark Industries. But an even deadlier foe is waiting... The Mandarin.

Mandarin has trouble win his son, Gene Khan, while trying to retrieve the rings. Tony Stark as Iron Man battles his invention that Obadiah transformed into a weapon. Mandarin steals the ring of Obadiah, and fights Iron Man. Back in Mandarin's lair it is revealed that Gene Khan has become The Mandarin.

Ivan Vanko, a scientist who was thought to have been left in space two years ago, crash lands in New York City. Alive because of an environmental suit, called the Crimson Dynamo, Vanko seeks revenge on the program that put him in space in the first place- Project Pegasus. It's up to Iron Man to stop Vanko from destroying Project Pegasus.

During the school science fair, Tony is approached by the leaders of an organization known as the Advanced Idea Mechanics. Offering up his help, Tony inadvertantly creates a new enemy, the Controller. With Tony's friends under its control, Iron Man must step in and save the day.